Contacts of the strand formed by residues 332 - 341 (chain B) in PDB entry 1SY7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.2 24.0 + - - +
107B SER 3.3 20.6 + - - -
108B ALA* 3.7 6.9 - - - +
110B ASP* 2.8 43.2 + - - -
111B LEU* 3.7 22.6 - - - +
301B GLY* 3.2 1.5 - - - -
302B ILE* 2.8 41.9 + - - +
330B PRO* 3.6 3.1 + - + +
331B VAL* 1.3 72.2 - - - +
333B TYR* 1.3 61.5 + - - +
334B ILE* 3.6 21.5 + - + +
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 3.3 25.4 + - - +
106B GLU* 4.0 8.0 - - - +
234B GLN* 4.6 3.3 + - - -
256B HIS* 4.7 5.4 + - + +
258B THR* 2.6 37.6 + - + +
299B LYS* 3.6 42.4 - - + +
300B PHE 3.3 6.1 - - - +
301B GLY* 3.5 24.9 - - - -
326B GLU* 5.3 2.2 + - - -
331B VAL* 3.5 32.9 + - + +
332B ARG* 1.3 73.1 - - - +
334B ILE* 1.3 63.1 + - - +
546B PHE* 4.9 4.3 - - - -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.3 20.5 - - + -
105B TYR* 2.7 35.6 + - - -
106B GLU* 3.2 25.9 + - + +
108B ALA* 3.7 24.9 - - + -
117B LEU* 4.4 4.9 - - + +
300B PHE* 2.9 22.8 + - + +
302B ILE* 3.7 21.5 - - + -
332B ARG* 3.7 38.6 - - + +
333B TYR* 1.3 79.9 - - - +
335B GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.5 0.9 - - - -
103B LYS 3.4 12.3 - - - -
104B VAL* 3.7 6.5 - - - -
105B TYR* 3.5 14.8 + - - -
299B LYS* 3.5 5.9 - - - +
300B PHE* 2.8 35.2 + - - +
334B ILE* 1.3 86.9 - - - +
336B GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS 4.1 0.2 - - - +
102B PHE* 3.5 7.0 - - - -
103B LYS* 3.0 34.4 + - - +
105B TYR* 4.7 11.0 - - + -
257B TRP* 5.2 0.2 - - - -
260B GLU* 2.5 37.1 - - - +
297B LYS* 3.7 19.4 - - + +
298B TRP 3.3 8.1 - - - +
299B LYS* 5.0 1.6 - - + -
300B PHE 4.6 0.4 - - - +
335B GLY* 1.3 74.8 - - - +
337B MET* 1.3 69.6 + - - +
338B GLU* 5.8 1.1 - - + +
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Residues in contact with MET 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS 3.3 13.5 - - - +
102B PHE* 4.0 5.8 - - + -
126B VAL* 4.1 10.8 - - + -
128B VAL* 3.8 26.7 - - + -
149B PHE* 3.9 26.5 - - + -
151B VAL* 4.0 11.4 - - - -
257B TRP* 3.5 37.2 - - + -
296B PRO 3.9 0.2 - - - +
297B LYS* 3.2 5.5 - - - +
298B TRP* 3.0 61.5 + - + +
336B GLU* 1.3 76.9 - - - +
338B GLU* 1.3 69.1 + - - +
339B LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY* 3.0 3.1 - - - -
101B LYS* 2.9 66.8 + - + +
295B TYR* 4.1 19.4 - - + +
296B PRO 3.2 11.0 - - - +
297B LYS* 3.4 35.0 + - + -
298B TRP* 5.3 0.2 - - - -
336B GLU* 5.8 1.6 - - + +
337B MET* 1.3 77.2 - - - +
339B LEU* 1.3 64.4 + - - +
340B ASN* 2.9 26.2 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 3.8 22.4 - - + +
99B PHE 3.4 10.8 - - - +
100B GLY* 4.1 2.2 - - - +
126B VAL* 4.5 2.9 - - + -
128B VAL* 3.6 29.8 - - + -
130B PHE* 3.6 36.3 - - + -
286B LEU* 4.3 10.5 - - + -
290B ILE* 3.8 12.9 - - + +
295B TYR* 3.2 20.1 - - - +
296B PRO* 3.1 23.4 + - + +
298B TRP* 4.0 17.5 - - + -
337B MET* 4.9 2.7 - - + -
338B GLU* 1.3 79.5 - - - +
340B ASN* 1.3 58.6 + - - +
341B ARG 3.9 0.7 - - - -
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Residues in contact with ASN 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 3.0 4.0 + - - +
100B GLY* 3.7 13.9 - - - -
101B LYS* 3.9 18.8 - - - +
290B ILE* 3.6 8.3 - - - +
295B TYR* 3.5 46.7 + - + -
338B GLU* 2.9 25.8 + - - +
339B LEU* 1.3 74.5 - - - +
341B ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 3.6 2.3 - - - +
99B PHE* 2.8 86.5 + - + +
290B ILE* 3.6 6.2 - - - +
339B LEU 3.9 0.2 - - - -
340B ASN* 1.3 90.6 - - - +
342B ASN* 1.3 72.4 + - - +
344B ASP* 4.0 20.4 + - - -
349B GLN* 5.2 0.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il